scholarly journals Prediction of Disease-related microRNAs through Integrating Attributes of microRNA Nodes and Multiple Kinds of Connecting Edges

Molecules ◽  
2019 ◽  
Vol 24 (17) ◽  
pp. 3099 ◽  
Author(s):  
Xuan ◽  
Li ◽  
Zhang ◽  
Zhang ◽  
Song
Keyword(s):  
State Of The Art ◽  
Dimensional Space ◽  
Nonnegative Matrix ◽  
Superior Performance ◽  
Pancreatic Cancers ◽  
Node Attribute ◽  
Disease Associations ◽  
Node Attributes ◽  
Novel Method ◽  
Low Dimensional

Identifying disease-associated microRNAs (disease miRNAs) contributes to the understanding of disease pathogenesis. Most previous computational biology studies focused on multiple kinds of connecting edges of miRNAs and diseases, including miRNA–miRNA similarities, disease–disease similarities, and miRNA–disease associations. Few methods exploited the node attribute information related to miRNA family and cluster. The previous methods do not completely consider the sparsity of node attributes. Additionally, it is challenging to deeply integrate the node attributes of miRNAs and the similarities and associations related to miRNAs and diseases. In the present study, we propose a novel method, known as MDAPred, based on nonnegative matrix factorization to predict candidate disease miRNAs. MDAPred integrates the node attributes of miRNAs and the related similarities and associations of miRNAs and diseases. Since a miRNA is typically subordinate to a family or a cluster, the node attributes of miRNAs are sparse. Similarly, the data for miRNA and disease similarities are sparse. Projecting the miRNA and disease similarities and miRNA node attributes into a common low-dimensional space contributes to estimating miRNA-disease associations. Simultaneously, the possibility that a miRNA is associated with a disease depends on the miRNA’s neighbour information. Therefore, MDAPred deeply integrates projections of multiple kinds of connecting edges, projections of miRNAs node attributes, and neighbour information of miRNAs. The cross-validation results showed that MDAPred achieved superior performance compared to other state-of-the-art methods for predicting disease-miRNA associations. MDAPred can also retrieve more actual miRNA-disease associations at the top of prediction results, which is very important for biologists. Additionally, case studies of breast, lung, and pancreatic cancers further confirmed the ability of MDAPred to discover potential miRNA–disease associations.

scholarly journals Network-Specific Variational Auto-Encoder for Embedding in Attribute Networks

2019 ◽  
Author(s):  
Di Jin ◽  
Bingyi Li ◽  
Pengfei Jiao ◽  
Dongxiao He ◽  
Weixiong Zhang
Keyword(s):  
Information Integration ◽  
Dimensional Space ◽  
Gaussian Mixture ◽  
Superior Performance ◽  
Network Structures ◽  
New Approach ◽  
Network Topologies ◽  
Node Attributes ◽  
Novel Method ◽  
Low Dimensional

Network embedding (NE) maps a network into a low-dimensional space while preserving intrinsic features of the network. Variational Auto-Encoder (VAE) has been actively studied for NE. These VAE-based methods typically utilize both network topologies and node semantics and treat these two types of data in the same way. However, the information of network topology and information of node semantics are orthogonal and are often from different sources; the former quantifies coupling relationships among nodes, whereas the latter represents node specific properties. Ignoring this difference affects NE. To address this issue, we develop a network-specific VAE for NE, named as NetVAE. In the encoding phase of our new approach, compression of network structures and compression of node attributes share the same encoder in order to perform co-training to achieve transfer learning and information integration. In the decoding phase, a dual decoder is introduced to reconstruct network topologies and node attributes separately. Specifically, as a part of the dual decoder, we develop a novel method based on a Gaussian mixture model and the block model to reconstruct network structures. Extensive experiments on large real-world networks demonstrate a superior performance of the new approach over the state-of-the-art methods.

scholarly journals Predicting miRNA-Disease Associations by Incorporating Projections in Low-Dimensional Space and Local Topological Information

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 685 ◽  
Author(s):  
Xuan ◽  
Zhang ◽  
Zhang ◽  
Li ◽  
Zhao
Keyword(s):  
Dimensional Space ◽  
Characteristic Curve ◽  
Feature Space ◽  
Superior Performance ◽  
Topological Information ◽  
Heterogeneous Information ◽  
Feature Representations ◽  
Disease Associations ◽  
Precision Recall Curve ◽  
Low Dimensional

Predicting the potential microRNA (miRNA) candidates associated with a disease helps in exploring the mechanisms of disease development. Most recent approaches have utilized heterogeneous information about miRNAs and diseases, including miRNA similarities, disease similarities, and miRNA-disease associations. However, these methods do not utilize the projections of miRNAs and diseases in a low-dimensional space. Thus, it is necessary to develop a method that can utilize the effective information in the low-dimensional space to predict potential disease-related miRNA candidates. We proposed a method based on non-negative matrix factorization, named DMAPred, to predict potential miRNA-disease associations. DMAPred exploits the similarities and associations of diseases and miRNAs, and it integrates local topological information of the miRNA network. The likelihood that a miRNA is associated with a disease also depends on their projections in low-dimensional space. Therefore, we project miRNAs and diseases into low-dimensional feature space to yield their low-dimensional and dense feature representations. Moreover, the sparse characteristic of miRNA-disease associations was introduced to make our predictive model more credible. DMAPred achieved superior performance for 15 well-characterized diseases with AUCs (area under the receiver operating characteristic curve) ranging from 0.860 to 0.973 and AUPRs (area under the precision-recall curve) ranging from 0.118 to 0.761. In addition, case studies on breast, prostatic, and lung neoplasms demonstrated the ability of DMAPred to discover potential disease-related miRNAs.

scholarly journals Convolutional Gaussian Embeddings for Personalized Recommendation with Uncertainty

2019 ◽  
Author(s):  
Junyang Jiang ◽  
Deqing Yang ◽  
Yanghua Xiao ◽  
Chenlu Shen
Keyword(s):  
State Of The Art ◽  
Dimensional Space ◽  
Monte Carlo Sampling ◽  
Superior Performance ◽  
Personalized Recommendation ◽  
Latent Features ◽  
Benchmark Datasets ◽  
Low Dimensional ◽  
Uncertain Preferences ◽  
Candidate Item

Most of existing embedding based recommendation models use embeddings (vectors) to represent users and items which contain latent features of users and items. Each of such embeddings corresponds to a single fixed point in low-dimensional space, thus fails to precisely represent the users/items with uncertainty which are often observed in recommender systems. Addressing this problem, we propose a unified deep recommendation framework employing Gaussian embeddings, which are proven adaptive to uncertain preferences exhibited by some users, resulting in better user representations and recommendation performance. Furthermore, our framework adopts Monte-Carlo sampling and convolutional neural networks to compute the correlation between the objective user and the candidate item, based on which precise recommendations are achieved. Our extensive experiments on two benchmark datasets not only justify that our proposed Gaussian embeddings capture the uncertainty of users very well, but also demonstrate its superior performance over the state-of-the-art recommendation models.

scholarly journals Season- and Trend-aware Symbolic Approximation for Accurate and Efficient Time Series Matching

2021 ◽  
Author(s):  
Lars Kegel ◽  
Claudio Hartmann ◽  
Maik Thiele ◽  
Wolfgang Lehner
Keyword(s):  
Time Series ◽  
State Of The Art ◽  
Dimensional Space ◽  
Symbolic Aggregate Approximation ◽  
Current State ◽  
Optimal Representation ◽  
Symbolic Approximation ◽  
Low Dimensional ◽  
Deterministic Behavior ◽  
Support Time

AbstractProcessing and analyzing time series datasets have become a central issue in many domains requiring data management systems to support time series as a native data type. A core access primitive of time series is matching, which requires efficient algorithms on-top of appropriate representations like the symbolic aggregate approximation (SAX) representing the current state of the art. This technique reduces a time series to a low-dimensional space by segmenting it and discretizing each segment into a small symbolic alphabet. Unfortunately, SAX ignores the deterministic behavior of time series such as cyclical repeating patterns or a trend component affecting all segments, which may lead to a sub-optimal representation accuracy. We therefore introduce a novel season- and a trend-aware symbolic approximation and demonstrate an improved representation accuracy without increasing the memory footprint. Most importantly, our techniques also enable a more efficient time series matching by providing a match up to three orders of magnitude faster than SAX.

Community detection in complex network by network embedding and density clustering

2021 ◽  
pp. 1-12
Author(s):  
JinFang Sheng ◽  
Huaiyu Zuo ◽  
Bin Wang ◽  
Qiong Li
Keyword(s):  
Complex Network ◽  
Community Detection ◽  
Dimensional Space ◽  
Detection Algorithm ◽  
Superior Performance ◽  
Network Embedding ◽  
Detection Algorithms ◽  
Density Clustering ◽  
Community Detection Algorithm ◽  
Low Dimensional

 In a complex network system, the structure of the network is an extremely important element for the analysis of the system, and the study of community detection algorithms is key to exploring the structure of the complex network. Traditional community detection algorithms would represent the network using an adjacency matrix based on observations, which may contain redundant information or noise that interferes with the detection results. In this paper, we propose a community detection algorithm based on density clustering. In order to improve the performance of density clustering, we consider an algorithmic framework for learning the continuous representation of network nodes in a low-dimensional space. The network structure is effectively preserved through network embedding, and density clustering is applied in the embedded low-dimensional space to compute the similarity of nodes in the network, which in turn reveals the implied structure in a given network. Experiments show that the algorithm has superior performance compared to other advanced community detection algorithms for real-world networks in multiple domains as well as synthetic networks, especially when the network data chaos is high.

scholarly journals DeepTable: a permutation invariant neural network for table orientation classification

2020 ◽  
Vol 34 (6) ◽  
pp. 1963-1983
Author(s):  
Maryam Habibi ◽  
Johannes Starlinger ◽  
Ulf Leser
Keyword(s):  
Deep Neural Networks ◽  
State Of The Art ◽  
Superior Performance ◽  
Web Pages ◽  
Specific Information ◽  
Silver Standard ◽  
Present Information ◽  
Previous State ◽  
Novel Method

Abstract Tables are a common way to present information in an intuitive and concise manner. They are used extensively in media such as scientific articles or web pages. Automatically analyzing the content of tables bears special challenges. One of the most basic tasks is determination of the orientation of a table: In column tables, columns represent one entity with the different attribute values present in the different rows; row tables are vice versa, and matrix tables give information on pairs of entities. In this paper, we address the problem of classifying a given table into one of the three layouts horizontal (for row tables), vertical (for column tables), and matrix. We describe DeepTable, a novel method based on deep neural networks designed for learning from sets. Contrary to previous state-of-the-art methods, this basis makes DeepTable invariant to the permutation of rows or columns, which is a highly desirable property as in most tables the order of rows and columns does not carry specific information. We evaluate our method using a silver standard corpus of 5500 tables extracted from biomedical articles where the layout was determined heuristically. DeepTable outperforms previous methods in both precision and recall on our corpus. In a second evaluation, we manually labeled a corpus of 300 tables and were able to confirm DeepTable to reach superior performance in the table layout classification task. The codes and resources introduced here are available at https://github.com/Marhabibi/DeepTable.

An anomaly detection method based on double encoder–decoder generative adversarial networks

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Hui Liu ◽  
Tinglong Tang ◽  
Jake Luo ◽  
Meng Zhao ◽  
Baole Zheng ◽  
...  
Keyword(s):  
Anomaly Detection ◽  
Latent Variables ◽  
Dimensional Space ◽  
Superior Performance ◽  
Generative Adversarial Networks ◽  
Training Process ◽  
Content Type ◽  
Detection Model ◽  
Adversarial Networks ◽  
Low Dimensional

Purpose This study aims to address the challenge of training a detection model for the robot to detect the abnormal samples in the industrial environment, while abnormal patterns are very rare under this condition. Design/methodology/approach The authors propose a new model with double encoder–decoder (DED) generative adversarial networks to detect anomalies when the model is trained without any abnormal patterns. The DED approach is used to map high-dimensional input images to a low-dimensional space, through which the latent variables are obtained. Minimizing the change in the latent variables during the training process helps the model learn the data distribution. Anomaly detection is achieved by calculating the distance between two low-dimensional vectors obtained from two encoders. Findings The proposed method has better accuracy and F1 score when compared with traditional anomaly detection models. Originality/value A new architecture with a DED pipeline is designed to capture the distribution of images in the training process so that anomalous samples are accurately identified. A new weight function is introduced to control the proportion of losses in the encoding reconstruction and adversarial phases to achieve better results. An anomaly detection model is proposed to achieve superior performance against prior state-of-the-art approaches.

scholarly journals Locally Linear Discriminate Embedding for Face Recognition

2009 ◽  
Vol 2009 ◽  
pp. 1-8 ◽  
Author(s):  
Eimad E. Abusham ◽  
E. K. Wong
Keyword(s):  
Face Recognition ◽  
Dimensional Space ◽  
Linear Structure ◽  
Data Representation ◽  
High Dimensional ◽  
Fast Processing ◽  
Novel Method ◽  
Computational Simplicity ◽  
Low Dimensional ◽  
Locally Linear

A novel method based on the local nonlinear mapping is presented in this research. The method is called Locally Linear Discriminate Embedding (LLDE). LLDE preserves a local linear structure of a high-dimensional space and obtains a compact data representation as accurately as possible in embedding space (low dimensional) before recognition. For computational simplicity and fast processing, Radial Basis Function (RBF) classifier is integrated with the LLDE. RBF classifier is carried out onto low-dimensional embedding with reference to the variance of the data. To validate the proposed method, CMU-PIE database has been used and experiments conducted in this research revealed the efficiency of the proposed methods in face recognition, as compared to the linear and non-linear approaches.

scholarly journals Unsupervised Deep Video Hashing with Balanced Rotation

2017 ◽  
Author(s):  
Gengshen Wu ◽  
Li Liu ◽  
Yuchen Guo ◽  
Guiguang Ding ◽  
Jungong Han ◽  
...  
Keyword(s):  
State Of The Art ◽  
Dimensional Space ◽  
Image Hashing ◽  
Neighborhood Structure ◽  
Function Learning ◽  
Video Hashing ◽  
Real World Datasets ◽  
Low Dimensional ◽  
Balanced Code ◽  
Hash Codes

Recently, hashing video contents for fast retrieval has received increasing attention due to the enormous growth of online videos. As the extension of image hashing techniques, traditional video hashing methods mainly focus on seeking the appropriate video features but pay little attention to how the video-specific features can be leveraged to achieve optimal binarization. In this paper, an end-to-end hashing framework, namely Unsupervised Deep Video Hashing (UDVH), is proposed, where feature extraction, balanced code learning and hash function learning are integrated and optimized in a self-taught manner. Particularly, distinguished from previous work, our framework enjoys two novelties: 1) an unsupervised hashing method that integrates the feature clustering and feature binarization, enabling the neighborhood structure to be preserved in the binary space; 2) a smart rotation applied to the video-specific features that are widely spread in the low-dimensional space such that the variance of dimensions can be balanced, thus generating more effective hash codes. Extensive experiments have been performed on two real-world datasets and the results demonstrate its superiority, compared to the state-of-the-art video hashing methods. To bootstrap further developments, the source code will be made publically available.

scholarly journals SCDRHA: A scRNA-Seq Data Dimensionality Reduction Algorithm Based on Hierarchical Autoencoder

2021 ◽  
Vol 12 ◽  
Author(s):  
Jianping Zhao ◽  
Na Wang ◽  
Haiyun Wang ◽  
Chunhou Zheng ◽  
Yansen Su
Keyword(s):  
Dimensionality Reduction ◽  
Data Visualization ◽  
State Of The Art ◽  
Dimensional Space ◽  
High Dimensional ◽  
Reduction Algorithm ◽  
Cell Clustering ◽  
Data Dimensionality Reduction ◽  
Single Cell Rna Sequencing ◽  
Low Dimensional

Dimensionality reduction of high-dimensional data is crucial for single-cell RNA sequencing (scRNA-seq) visualization and clustering. One prominent challenge in scRNA-seq studies comes from the dropout events, which lead to zero-inflated data. To address this issue, in this paper, we propose a scRNA-seq data dimensionality reduction algorithm based on a hierarchical autoencoder, termed SCDRHA. The proposed SCDRHA consists of two core modules, where the first module is a deep count autoencoder (DCA) that is used to denoise data, and the second module is a graph autoencoder that projects the data into a low-dimensional space. Experimental results demonstrate that SCDRHA has better performance than existing state-of-the-art algorithms on dimension reduction and noise reduction in five real scRNA-seq datasets. Besides, SCDRHA can also dramatically improve the performance of data visualization and cell clustering.

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